From bb4dad72aa4b1e2ddf9bf521b1bcb5b2f21c01d9 Mon Sep 17 00:00:00 2001
From: Umar Yousafzai <39500143+uyousafzai54@users.noreply.github.com>
Date: Fri, 2 Jun 2023 15:00:36 -0400
Subject: [PATCH 1/3] add stop_before_pixels tag and set to True to speed up
 dcm reads (#80)

AYE AYE
---
 imgtools/utils/crawl.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/imgtools/utils/crawl.py b/imgtools/utils/crawl.py
index 732691d..666fb4d 100644
--- a/imgtools/utils/crawl.py
+++ b/imgtools/utils/crawl.py
@@ -25,7 +25,7 @@ def crawl_one(folder):
                 rel_path  = dcm_path.relative_to(folder_path.parent.parent)                                        # rel_path of dicom from folder
                 rel_posix = rel_path.parent.as_posix()     # folder name + until parent folder of dicom
 
-                meta      = dcmread(dcm, force=True)
+                meta      = dcmread(dcm, force=True, stop_before_pixels=True)
                 patient   = str(meta.PatientID)
                 study     = str(meta.StudyInstanceUID)
                 series    = str(meta.SeriesInstanceUID)

From 1268cbc668d2960e3dbb66955ed84b298bb1a651 Mon Sep 17 00:00:00 2001
From: Sejin Kim <40668167+skim2257@users.noreply.github.com>
Date: Fri, 2 Jun 2023 15:03:48 -0400
Subject: [PATCH 2/3] test break during demo (#81)

* test break during demo
- changed https://github.com/bhklab/med-imagetools/blob/d99950f4240ec286deeef6d635fe329ca520f2a7/imgtools/modules/datagraph.py#L61 set 2nd half pandas`astype(str)`

* Update setup.py to 1.1.6
---
 imgtools/modules/datagraph.py | 2 +-
 setup.py                      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/imgtools/modules/datagraph.py b/imgtools/modules/datagraph.py
index 81821fd..5caf0db 100644
--- a/imgtools/modules/datagraph.py
+++ b/imgtools/modules/datagraph.py
@@ -58,7 +58,7 @@ def form_graph(self):
             self.df[col] = self.df[col].astype(str)
         
         #Get reference_rs information from RTDOSE-RTPLAN connections    
-        df_filter = pd.merge(self.df, self.df[["instance_uid","reference_rs"]], 
+        df_filter = pd.merge(self.df, self.df[["instance_uid","reference_rs"]].apply(lambda x: x.astype(str), axis=1), 
                              left_on="reference_pl", 
                              right_on="instance_uid", 
                              how="left")
diff --git a/setup.py b/setup.py
index 18b13ef..aaf1cfc 100644
--- a/setup.py
+++ b/setup.py
@@ -8,7 +8,7 @@
     
 setup(
     name="med-imagetools",
-    version="1.1.5",
+    version="1.1.6",
     author="Sejin Kim, Michal Kazmierski, Kevin Qu, Vishwesh Ramanathan, Benjamin Haibe-Kains",
     author_email="benjamin.haibe.kains@utoronto.ca",
     description="Transparent and reproducible image processing pipelines in Python.",

From ba50037fee4c0c6bc0640d5efdc074ea75944da7 Mon Sep 17 00:00:00 2001
From: RuiyanNi <91274748+RuiyanNi@users.noreply.github.com>
Date: Fri, 16 Jun 2023 15:02:03 -0400
Subject: [PATCH 3/3] convert to dicom (#89)

nifti to dicom function
---
 imgtools/utils/nifti_to_dicom.py | 46 ++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 imgtools/utils/nifti_to_dicom.py

diff --git a/imgtools/utils/nifti_to_dicom.py b/imgtools/utils/nifti_to_dicom.py
new file mode 100644
index 0000000..0cf9d2b
--- /dev/null
+++ b/imgtools/utils/nifti_to_dicom.py
@@ -0,0 +1,46 @@
+import SimpleITK as sitk
+from rt_utils import RTStructBuilder
+import pydicom
+import logging
+import glob
+import numpy as np
+import os
+
+'''You need to install rt_utils first using 
+    pip install rt_utils'''
+
+
+def segmentations_to_dicom(save_path:str,orig_series_info:dict, segmentation:sitk.Image,segmentations_labels:dict,
+                             color_list=None, rtstruct_basefilename='rtstruct.dcm'):
+    """
+    This function takes a list of the original dicom data, moves it to the save_path and creates a corresponding rt_struct
+    @param image_set_name: name of the image set used to create the dicom sub directory
+    @param save_path: directory to save dicom data
+    @param orig_series_info: original series info see @get_dicom_series_dict_pyd
+    @param segmentation: the image containing integer segmentation data
+    @param segmentations_labels: a dictionary with segmentation label information mapping ints in @segmentation to label
+    name e.g. {1: 'Bladder', 2: 'Rectum', 3: 'Sigmoid', 4: 'SmallBowel'}
+    @return:
+    """
+    _logger=logging.getLogger(__name__)
+    #make output dir
+    if not os.path.isdir(save_path):
+        _logger.warning(f'Making path: {save_path}')
+        os.makedirs(save_path)
+
+
+    im_array = sitk.GetArrayFromImage(segmentation)
+    rtstruct = RTStructBuilder.create_new(dicom_series_path=orig_series_info)
+    for i,(key,name) in enumerate(segmentations_labels.items()):
+        mask = np.where(im_array!=key,0,im_array)
+        mask = np.array(mask,dtype=bool)
+        mask = np.transpose(mask, (1,2,0))
+
+        index = i%len(color_list)
+
+        rtstruct.add_roi(mask=mask, name=name, color=color_list[index],approximate_contours=False)
+
+
+    rtstruct_name = os.path.join(save_path,rtstruct_basefilename)
+    _logger.info(f'Saving rtstruct data: {rtstruct_name}')
+    rtstruct.save(rtstruct_name)